Project Plan
pyrad$volume = as.numeric(pyrad$lesion1sizepath)
pyrad$volume_from_pyrad = as.numeric(pyrad$original_shape_MeshVolume)
pyrad$diameter = as.numeric(pyrad$original_shape_Maximum2DDiameterSlice)
pyrad$radITH = rowMeans(pyrad[,features_of_interest], na.rm = T)
Q = 3
pyrad$volume_group = gtools::quantcut(pyrad$volume, q=Q, na.rm=TRUE)
pyrad$diameter_group = gtools::quantcut(pyrad$diameter, q=Q, na.rm=TRUE)
pyrad$radITH_group = gtools::quantcut(pyrad$radITH, q=Q, na.rm=TRUE)
Let’s group DRIVER mutations by Sanchez Vega def
## [1] "Adeno fisher test results"
## [1] "nrf2"
##
## Fisher's Exact Test for Count Data
##
## data: table(tmp$radITH_group, tmp[, col])
## p-value = 0.02679
## alternative hypothesis: two.sided
##
## [1] "pi3k"
##
## Fisher's Exact Test for Count Data
##
## data: table(tmp$radITH_group, tmp[, col])
## p-value = 0.003382
## alternative hypothesis: two.sided
##
## [1] "cell_cycle"
##
## Fisher's Exact Test for Count Data
##
## data: table(tmp$radITH_group, tmp[, col])
## p-value = 0.0003902
## alternative hypothesis: two.sided
##
## [1] "wnt"
##
## Fisher's Exact Test for Count Data
##
## data: table(tmp$radITH_group, tmp[, col])
## p-value = 0.04017
## alternative hypothesis: two.sided
## [1] "Squamous fisher test results"
## [1] "rtk_kras"
##
## Fisher's Exact Test for Count Data
##
## data: table(tmp$radITH_group, tmp[, col])
## p-value = 0.01748
## alternative hypothesis: two.sided
##
## [1] "pi3k"
##
## Fisher's Exact Test for Count Data
##
## data: table(tmp$radITH_group, tmp[, col])
## p-value = 0.007167
## alternative hypothesis: two.sided
## [1] "Adeno fisher test results"
## [1] "Squamous fisher test results"
## [1] "hippo"
##
## Fisher's Exact Test for Count Data
##
## data: table(tmp$volume_group, tmp[, col])
## p-value = 0.01164
## alternative hypothesis: two.sided
## Number of Genes after cutoff: 10332